Failing test for YuLab-SMU#282

Issue is that match.call doesn't capture default arguments. See https://stackoverflow.com/questions/14397364/match-call-with-default-arguments

tests/testthat/test-compareCluster.R

@@ -0,0 +1,32 @@
+context("Test compareCluster")
+
+data(gcSample)
+gc_small = gcSample[c("X1", "X2", 'X4')]
+test_that("compareCluster + KEGG no formula", {
+result = compareCluster(gc_small, fun="enrichKEGG",
+                      organism="hsa", pvalueCutoff=0.05)
+expect_is(result, 'compareClusterResult')
+})
+
+
+test_that("compareCluster + KEGG + formula", {
+  gc_small_dat = do.call(rbind,
+                         lapply(names(gc_small),
+                                function(x) data.frame(X = x, entrezID = gc_small[[x]], stringsAsFactors = FALSE)
+                                ))
+  result = compareCluster(entrezID ~ X, data = gc_small_dat, fun="enrichKEGG",
+                          organism="hsa", pvalueCutoff=0.05)
+  expect_is(result, 'compareClusterResult')
+})
+
+test_that("compareCluster + GO no formula", {
+  result = compareCluster(gc_small, fun="enrichGO", OrgDb = "org.Hs.eg.db",
+                          pvalueCutoff=0.05)
+  expect_is(result, 'compareClusterResult')
+})
+
+test_that("compareCluster + GO no formula, default value for function", {
+  result = compareCluster(gc_small, OrgDb = "org.Hs.eg.db",
+                          pvalueCutoff=0.05)
+  expect_is(result, 'compareClusterResult')
+})

tests/testthat/test-extract_params.R

@@ -0,0 +1,22 @@
+context("Test extract_params")
+
+test_function = function(x, y, z = 'z'){
+  this_call = match.call(expand.dots = TRUE)
+  return(extract_params(this_call))
+}
+
+test_that("Can extract position parameters", {
+  params = test_function(1, 2, 3)
+  expect_equal(params, list(x = "1", y = "2", z = "3"))
+  # note these are coerced to character, might not be desirable..
+})
+
+test_that("Can extract keyword parameters", {
+  params = test_function(x = 1, z = 3, y = 2)
+  expect_equal(params, list(x = "1", y = "2", z = "3"))
+})
+
+test_that("Can extract default parameters", {
+  params = test_function(x = 1, y = 2)
+  expect_equal(params, list(x = "1", y = "2", z = "z"))
+})